Urban spatial structure is an important part of the research on the regional system of the human-land relationship, and it is also an important starting point for the sustainable development of cities. How to scientifically understand the urban spatial structure in the new era is the basis for optimizing its regulation. This study briefly reviews the historical background of traditional urban spatial structure theory and points out the transformational turn of urban spatial structure in terms of organizational principles, organizational methods, optimization goals and elements through the analysis of technological revolution, policy, and socio-economic environment in the new era, and clarifies the limitations of traditional urban structure theory in explaining urban structure in the new era. This study proposes a path for understanding urban spatial structure in the new era, including reconstructing the research paradigm of urban spatial structure from the theory of human-land territorial system, re-understanding the carrier space of urban spatial structure, strengthening the analysis of urban structure relationship, and innovating the measurement system of urban spatial structure. The key measures to deal with the challenges of urban spatial structure cognition in the future, namely, reconstructing the theory of urban spatial structure, integrating key technologies of urban spatial structure analysis, integrating and apply multi-source data and building a digital twin platform for urban spatial structure optimization and regulation.